Considerations for Designing a UTI Panel

Urinary tract infections (UTIs) are common infections that occur when bacteria or yeast enter the urinary tract. These infections can cause pelvic pain, frequent urination, urgency, or abnormal dark or strong-smelling urine. These infections frequently re-occur in patients after antibiotic treatment and can be challenging to treat.^1,2,3 Laboratories can detect the presence of bacteria in the urine of patients with UTI infections by using various diagnostic tests, including standard urine culture (SUC), direct microscopy, and, most recently, molecular technologies such as Polymerase Chain Reaction (PCR) and reverse transcription Polymerase Chain Reaction (RT-PCR). Scientists perform these laboratory tests to detect and identify the pathogens causing UTIs. However, these diagnostic tests vary in how scientists perform these tests, the limitations of the test, and the level of possible error of testing results.^4,5

Many in vitro diagnostic (IVD) tests are available that incorporate molecular technologies offering high levels of sensitivity and specificity to detect many uropathogens identified in UTI infections. Laboratories can either purchase a premade FDA-approved IVD test from a manufacturer or may want to develop their own in-house laboratory-developed test (LDT) to aid in detecting and identifying these specific organisms. Uropathogens that cause a UTI can be bacterial or fungal and can occur as a monomicrobial or polymicrobial infection.^6,7 Multiplex PCR technology is not limited to detecting a single pathogen but can simultaneously test numerous pathogens and detect the presence of antibiotic resistance in one test. Molecular technologies can produce same-day patient results, which enables a reduction of reliance on empiric therapy for treating UTIs. A few common uropathogens identified by laboratory testing that are known to cause a UTI infection are:

Escherichia coli              Proteus mirabilis           Enterococcus spp.

Klebsiella pneumoniae   Enterobacter faecalis     Staphylococcus saprophyticus^8,9,10

There are many other uropathogens that can be considered to include in the panel at the discretion of the scientific staff or prevalence in regional testing.

A starting point when designing a molecular UTI panel is the identification of the pathogens scientists will include in the testing panel. Performing publication and evidence research on UTI pathogens

in the scientific literature and testing is essential to forming a solid laboratory testing menu. There is vast scientific literature on the common bacteria identified in urinary tract infections. Once the scientific staff creates a draft testing menu, scientists should also conduct a literature search of current UTI pathogens and diagnostic techniques to understand which pathogens they should add to the testing panel and their clinical significance. Laboratories will need to read about common bacteria, fungi, and any new pathogens that may be of interest in a proposed assay. Surveying other UTI panels offered by other laboratories will also give scientists insight into standard clinically relevant uropathogens, including some optional analytes to include in their menu. By performing careful and extensive research into the pathogens relevant to UTI infections in past and current literature, combined with information from existing UTI panels, scientists can formulate a robust and clinically helpful diagnostic test to offer providers.

Once a group of UTI pathogens has been identified as clinically relevant for a UTI test menu, the laboratory will need to decide if they would like to purchase an in vitro diagnostic (IVD) test or validate their own laboratory-developed test (LDT). An IVD test is a predesigned test that is sold to laboratories that has received FDA approval and has been examined for its clinical and analytical validity. An LDT is a test that is designed by the laboratories itself and must be internally validated for its analytical validity before it can be offered to the public.

Once the laboratory decides whether it will select an IVD test or choose to design their own UTI LDT, the next step is to validate the test in the laboratory. Validation of a testing panel is necessary to evaluate the IVD or LDT for its reproducibility, accuracy, and its use in a clinical patient setting. A validation team drafts the validation plan in which the laboratory will perform testing using the protocols designed to determine the accuracy, precision, linearity, analytical sensitivity, analytical specificity/selectivity, and test accuracy. A UTI testing validation plan will contain the following:

1)         A list of pathogen targets (bacteria, viral, and fungal) to be identified, including a list of sequences to be detected by M-PCR;
2)         The antibiotic resistance (ABR) genes and their sequences to be detected by M-PCR;
3)         Equipment list of what the scientific staff will use in the testing protocol;
4)         List of reagents;
5)         Specimen types such as urine, either clean catch or catheterized urine;
6)         Testing protocols that the validation team will follow to perform the test;
7)         Quality control is required for each test and should include positive, negative, and internal (IC) controls;
8)         The validation team will evaluate method performance and experimental design during the validation process. There are some differences between an IVD and LDT for the validation requirements. For an LDT test, this section will calculate the accuracy, precision, linearity, analytical sensitivity, analytical specificity/selectivity, and reportable range using the samples used for the validation. For an IVD test, validation studies should calculate accuracy, precision, and the reportable range (for quantitative assays). Analytical sensitivity (LOD) may also be necessary to perform quantitative assays by the College of American Pathology (CAP);¹¹
9)         Stability studies determine how specimens will be collected and processed by the laboratory to ensure the quality and reproducibility of the test;^12,13
10)       Clinical validation understanding limitations of the test with real-world clinical samples should follow analytical validation.

Once the Laboratory Director completes and approves a validation plan, the laboratory staff will evaluate the IVD or LDT before the laboratory can offer the test to the public.

Careful consideration of the reimbursement landscape is critical before offering a new molecular UTI assay to the public. Once a validated test is ready to be provided to the public, the laboratory should analyze both commercial private insurance payer coverage policies, Medicare and Medicaid National Coverage Determination (NCD), and Local Coverage Determination (LCD) to understand to assess the clinical need for the test. If molecular detection of specific bacteria exists in the current payer coverage policies, it will be easier for the laboratory to receive reimbursement for performing the test.^14,15 If a pathogen is not specified in payor policies or the policies do not support coverage, it may take a significant generation of evidence to support payor coverage of these pathogens. It is also crucial for the laboratory staff to review the standard policies of current UTI testing, such as standard urine culture (SUC) or immunoassays, and compare these policies to the new molecular UTI test being developed. By comparing the policies surrounding a new UTI assay to the existing testing methods, scientists can discuss how it will increase the quality of current testing methods and support insurance coverage and payment for the new test.

Once a laboratory offers a new molecular UTI panel, it is imperative to continue to survey its performance in the clinical testing environment. There may also be some changes needed to the bacteria analytes in the assay. From the time of development until its use by physicians, some pathogens may not be detected by the test, while others are emerging in the scientific literature or published studies. In this case, the laboratory may want to add or remove these pathogens from the testing menu. Scientific staff should constantly evaluate the existing test on its performance and how it is reporting these values to the public. Feedback from physicians using the test is essential for insights into the value of the assay for their patients and treatment plans. The laboratory should also be reviewing medical policies governing the test and working with payors to optimize utilization. It also may be helpful to consider studies demonstrating the increased specificity and sensitivity of the PCR test compared to the other testing methods for detecting UTI pathogens. The laboratory and staff should monitor successful molecular infectious disease panels for their usefulness and update the testing menu as needed.

Thoughtful and careful planning and execution are needed to design a UTI test that incorporates molecular technology to offer to the public. The assay development begins with researching the bacteria to be included in the panel, validating the UTI test, and understanding the reimbursement from payers of the test. Considering each step in developing a UTI test that incorporates molecular technology is necessary to offer a comprehensive and clinically relevant test that will succeed in commercial clinical laboratories.

Watch Our On-Demand webinar: How to Choose Clinically Relevant Targets for Your Infectious Disease Panels.

About the Author

Dr. Margo Lee is a dedicated Senior Medical Science Liaison with over a decade of experience supporting molecular clinical diagnostics in the fields of infectious disease and genetic testing. She has worked for many years both in Medical Affairs and as a laboratory scientist. Dr. Lee is driven by the need to share her clinical and laboratory expertise with the medical community and to help improve patient outcomes. Dr. Lee has worked at the National Institutes of Health, both at the National Cancer Institute and Human Genome Research Institute.

References:

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